Structure of PDB 1g32 Chain B Binding Site BS03

Receptor Information
>1g32 Chain B (length=252) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IVEGSDAEIGMSPWQVMLFRKSPQELLCGASLISDRWVLTAAHCLLYPPW
DKNFTENDLLVRIGKHSRTRYERNIEKISMLEKIYIHPRYNWRENLDRDI
ALMKLKKPVAFSDYIHPVCLPDRETAASLLQAGYKGRVTGWGNLKETGQP
SVLQVVNLPIVERPVCKDSTRIRITDNMFCAGYKPDEGKRGDACEGDSGG
PFVMKSPFNNRWYQMGIVSWGEGCDRDGKYGFYTHVFRLKKWIQKVIDQF
GE
Ligand information
Ligand IDR11
InChIInChI=1S/C25H25N7/c1-16-29-20-5-3-4-6-23(20)32(16)15-17-7-12-22-21(13-17)30-24(31(22)2)14-28-19-10-8-18(9-11-19)25(26)27/h3-13,28H,14-15H2,1-2H3,(H3,26,27)
InChIKeyIRKPNOLLMNHSOU-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cn1c(CNc2ccc(cc2)C(N)=N)nc3cc(Cn4c(C)nc5ccccc45)ccc13
OpenEye OEToolkits 1.5.0[H]/N=C(/c1ccc(cc1)NCc2nc3cc(ccc3n2C)Cn4c(nc5c4cccc5)C)\N
ACDLabs 10.04[N@H]=C(N)c1ccc(cc1)NCc3nc2cc(ccc2n3C)Cn4c5ccccc5nc4C
OpenEye OEToolkits 1.5.0[H]N=C(c1ccc(cc1)NCc2nc3cc(ccc3n2C)Cn4c(nc5c4cccc5)C)N
FormulaC25 H25 N7
Name4-{[1-METHYL-5-(2-METHYL-BENZOIMIDAZOL-1-YLMETHYL)-1H-BENZOIMIDAZOL-2-YLMETHYL]-AMINO}-BENZAMIDINE
ChEMBL
DrugBankDB02354
ZINCZINC000000591050
PDB chain1g32 Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1g32 Structural basis for inhibition promiscuity of dual specific thrombin and factor Xa blood coagulation inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		H57 Y60A W60D N98 L99 I174 D189 A190 S195 S214 W215 G216
Binding residue
(residue number reindexed from 1)		H43 Y47 W50 N95 L96 I172 D192 A193 S198 S219 W220 G221
Annotation score1
Binding affinityMOAD: Ki=780nM
PDBbind-CN: -logKd/Ki=6.11,Ki=780nM
BindingDB: Ki=780nM
Enzymatic activity
Catalytic site (original residue number in PDB) H57 D102 E192 G193 D194 S195 G196
Catalytic site (residue number reindexed from 1) H43 D99 E195 G196 D197 S198 G199
Enzyme Commision number 3.4.21.5: thrombin.
Gene Ontology
Molecular Function
GO:0004252 serine-type endopeptidase activity
GO:0005509 calcium ion binding
Biological Process
GO:0006508 proteolysis
GO:0007596 blood coagulation

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1g32, PDBe:1g32, PDBj:1g32
PDBsum1g32
PubMed11342132
UniProtP00734|THRB_HUMAN Prothrombin (Gene Name=F2)

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